Tracking Git commits

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Core commits

Recent Commits to bioperl-live:master

Merge branch 'master' of
Add to documentation, reorganize code a bit
spiced_seq() may need LWP
fix a warning in "_read_GenBank_Species", adjusted a regex to
Location/Split: Added its own "length" subroutine to
Fixing a change to a method name that works (_notes_file doesn't exist, _notes_path does)
Reverting the behavor of the index_dir method to silently do nothing if it doesn't find files to index, making it work with GFF files without fasta again.
(Thomas Sibley): Tell Storable to freeze and thaw CODE refs
Clean up and move to proper spot
Add tsibley's work to Changes file
Let Data::Dumper deparse CODE refs to serialize them, just like Storable
Localize Storable options instead of enabling them globally
Splicedseq.t: Reorganized new tests to use "-requires_networking"
Add tests for spliced_seq remote sequence handling
Fixed bug: too many Ns added by spliced_seq
Revert "Move out of Root into an install-specific directory; this will"
Move out of Root into an install-specific directory; this will
change default BLAST URL per Scott McGinnis at NCBI
SeqFeature/Location.t: Added tests for GitHub issue #71 fix
Run commits

Recent Commits to bioperl-run:master

POD updates
Really die if EMBOSS is not found
I'm not sure if these programs will run on Windows now
Windows use 'NUL' instead of '/dev/null', so added the option
Added a way to find the required files in Windows using "dir"
Hmmer: Prevent errors caused by the presence of whitespace
Bowtie.t: "qx/ulimit -n 3>&-/" does not work as intended on Windows; In "reset_parameters", added an intermediary hash
BWA.t, Bowtie.t, Maq.t & Samtools.t: Moved tests using
AnalysisFactory_soap.t & Analysis_soap.t: Changed tests to 0.
Build.PL & MYMETA.json: Added SOAP::Lite v0.716 in
SoapEU-function.t: Updated expected version of a genome to current Some temporal files were not deleted
SABlastPlus.t: Added an additional $fac->cleanup for
SABlastPlus.t: Some bl2seq tests were giving hits even when the
Vista.t: The 'java Vista 2>&1' command to determine if Vista
FastTree.t & Neighbor.t: Fixed number of skipped tests and removed
BEDTools.t: Moved the file-finding lines inside the SKIP block,
Blat.t: Fixed skipped tests number and removed "$blat_present",
Hyphy/ Changed @validvals[$i] to $validvals[$i].
Ext commits

Recent Commits to bioperl-ext:master

moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet
use UPPPER_TOL to catch the case when the expectation maximization step
fixed Vitebi typo
Fixed the typemap and also a memory bug in viterbi function in HMM.xs
adding FEEDBACK:Support section to pod
Bump to 1.007 (similar to trunk)
ext patches (courtesy Thomas Jahns)
get rid of some unended comment warnings from C compiler
-fPIC needed for lib construction
include errno definition
removed DEBUG=1
IUPAC DNA support
IUPAC DNA test case
Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?
Add cast to correct pointer type (get rid of warnings)
update version to last bioperl release
bug 2329
bug 2074/2329
Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this?
bug 2074
Bioperl-DB (BioSQL)

Recent Commits to bioperl-db:master

Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
buzgilla -> redmine
[RT 44466] remove corba-related scripts, now obsolete
squash perl 5.12 warning
ignore conf file
add minimal .gitignore file
weird duplication removed
committing patch for bug #2958
test commit to check SVN::Notify
Build.PL now checks for DBD drivers and attempts to DTRT
update Changes
fix empty POD section
some pod cleaning
main trunk version is wrong
* 02species.t now compared to similarly behaving instance, also creates comparable array
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